Different propeller has different shaft frequency. Shaft frequency is one character of the target which can be applied to underwater targets identification. In this paper, a method to improve the DEMON spectrum estimation is proposed and by which we can get a DEMON spectrum which has only distinct line-spectrums. We then present the largest common divisor algorithm and give the process of extracting shaft frequency. The result of sea experiment shows that the method and the algorithm proposed are effective and feasible.